degPatterns error about degreport HOT 8 OPEN

Hi @wangmhan ,

Can you post the exact error you get? If you try the example in the man page, does it work?

If you paste here all the output when you run it, I may able to see what is happening.

Thanks!

from degreport.

Hi,

I tried the example, it also cannot work with consensusCluster = TRUE.

The code is like this:
library("DEGreport")

data(humanGender)
library(SummarizedExperiment)
library(ggplot2)
ma <- assays(humanGender)[[1]][1:100,]
des <- colData(humanGender)
des[["other"]] <- sample(c("a", "b"), 85, replace = TRUE)
res <- degPatterns(ma, des, time="group", col = "other",consensusCluster = TRUE)

And the error report is:
Working with 100 genes.
end fraction
Error in frame() : figure margins too large

Did I misunderstand end fraction as error? But it cannot get the plot of cluster as usual.

from degreport.

I see, are you using R studio, this happens in general when the Panel for figures is too small. Can you try to increase the size of that panel? It is working for me.

If you are not using R studio, let me know.

Cheers

from degreport.

from degreport.

Hi,
I tried the example,
The code is like this:

library("DEGreport")
data(humanGender)
library(SummarizedExperiment)
library(ggplot2)
ma <- assays(humanGender)[[1]][1:100,]
des <- colData(humanGender)
des[["other"]] <- sample(c("a", "b"), 85, replace = TRUE)
res <- degPatterns(ma, des, time="group", col = "other",consensusCluster = TRUE)

And the error report is:
Working with 100 genes.
Working with 63 genes after filtering: minc > 15
Joining, by = "merge"
error: Problem with summarise() input n_genes.
x could not find function "n"
i Input n_genes is n().
i The error occurred in group 1: merge = "aFemale", cluster = 1, group = "Female", other = "a".
Run rlang::last_error() to see where the error occurred.

and I ran rlang::last_error() with this result

rlang::last_error()
<error/dplyr_error>
Problem with summarise() input n_genes.
x could not find function "n"
i Input n_genes is n().
i The error occurred in group 1: merge = "aFemale", cluster = 1, group = "Female", other = "a".
Backtrace:

1. DEGreport::degPatterns(...)
2. base::.handleSimpleError(...)
3. dplyr:::h(simpleError(msg, call))
   Run rlang::last_trace() to see the full context.

from degreport.

Hi, Thanks for reporting this.
Can you tell me the version of the package and R/Bioconductor you are using?

from degreport.

Thanks for your reply.
I run example in Rstudio Version 1.2.5033 and R version 4.0.3.
My DEGreport is version 1.25.3 and installed by remotes .

remotes::install_github("lpantano/DEGreport")

All packages were updated during the installation.

from degreport.

Hi,

I was able to reproduce when installing from github, I am trying to fix this.

Can you trying installation directly from Bioconductor:

BiocManager::install("DEGreport")

Thanks!

from degreport.